SARS-ANI: a global open access dataset of reported SARS-CoV-2 events in animals

The zoonotic origin of SARS-CoV-2, the etiological agent of COVID-19, is not yet fully resolved. Although natural infections in animals are reported in a wide range of species, large knowledge and data gaps remain regarding SARS-CoV-2 in animal hosts. We used two major health databases to extract unstructured data and generated a global dataset of SARS-CoV-2 events in animals. The dataset presents harmonized host names, integrates relevant epidemiological and clinical data on each event, and is readily usable for analytical purposes. We also share the code for technical and visual validation of the data and created a user-friendly dashboard for data exploration. Data on SARS-CoV-2 occurrence in animals is critical to adapting monitoring strategies, preventing the formation of animal reservoirs, and tailoring future human and animal vaccination programs. The FAIRness and analytical flexibility of the data will support research efforts on SARS-CoV-2 at the human-animal-environment interface. We intend to update this dataset weekly for at least one year and, through collaborations, to develop it further and expand its use.


Example 1
The two following SARS-CoV-2 animal events occurred in the United States (country_name), in one household (living_conditions = pet AND event 2 is related to event 1, see related_to_other_entries = "living together") where three dogs were living (number_susceptible = 3). The first dog was tested by PCR (test = PCR) because it had contact with a human diagnosed with COVID-19 (reason_for_testing = confirmed human case); the infection was confirmed on 2020-06-25 (date_confirmed): the dog showed symptoms that were not related to SARS-CoV-2 infection (symptoms = unrelated symptoms) and died from a cause not related to its SARS-CoV-2 status (outcome = death not related to . This case was reported (date_reported) on 2020-07-02 by the WAHIS.
Almost two months later (date_reported = 2020-08-27), a second dog of this household (counting at that time two dogs, number_susceptible = 2) which had contact with the dog described in event 1 (related_to_other_entries = living together AND reason_for_testing = confirmed animal case) was tested for SARS-CoV-2 by virus neutralization test (test). The dog was asymptomatic (symptoms = subclinical) and was isolated (control_measures). Outcome of the infection was not reported (outcome = NS).
Summary: These events describe one outbreak of SARS-CoV-2 in a multi-dog household following contact with a COVID-19-infected person and in which 2/3 dogs were infected (for clarity purpose, not all fields of the dataset are shown below). The three following events occurred in a zoo ( For the three other animals described in event 5, the outcome of the infection is reported (outcome = improved condition). Because these three tigers were reported together and showed the same event and patients attributes (e.g. date_reported, test, outcome), they are entered as one event in the dataset (epidemiological_unit = group).
Summary: These three events describe one outbreak (occurrence of one or more cases in an epidemiological unit, which is here the enclosure of the tigers in the zoo), which started on 2020-04-03 and included five cases of SARS-CoV-2 infection (for clarity purpose, not all fields of the dataset are shown below). The three following events report an outbreak that occurred in free ranging (living_conditions = wildlife) white-tailed deer (host_com_res) in Canada (country) that were tested during a surveillance/monitoring programme (reason_for_testing). The animals were sampled as part of the same epidemiological investigation but not necessary at the same geographic location (epidemiological_unit = survey group). Event 7 is an update of (related_to_other_entries) event 6 (related_to_other_entries = update by) and event 8 (related to event 7, see below) should also be considered as an update of event 6.
Events 6 and 7 report infections in more than one animal (epidemiological_unit = survey group) while event 8 reports infection in one single animal (epidemiological_unit = animal) related to the group described in event 7 (related_to_other_entries = same study). Event 7 and 8 are distinguished because the tests conducted in the animal in event 8 differed from those performed on the four animals described in event 7.
Date at which infection was confirmed (date_confirmed) is not specified in any events (NS); only event 6 was reported by the WAHIS (date_reported = 2022-01-20). The follow-up events (events 7 and 8) were published ~1.5 month after event 6. Most likely, this difference is due to the time required for laboratory analyses (events 7 and 8 present more sample and test types and provide identification of the SARS-CoV-2 variant involved).
Summary: These three events describe one outbreak (occurrence of one or more cases in an epidemiological unit, which is here the surveyed animals) which was reported for the first time by WAHIS and published on 2022-01-20 and was subsequently updated on 2022-03-03 in ProMED-mail, probably following more laboratory investigations. The outbreak included five confirmed cases of SARS-CoV-2 in white-tailed deer in Canada. The five animals did not die following SARS-CoV-2 infection (number_deaths = 0 AND outcome = death not related to Sars-CoV-2). Indeed, they died from hunting, which this is not specified in the dataset but can be found in the reports (for clarity purpose, not all fields of the dataset are shown below).